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BioC 3.4: CHECK report for chroGPS on moscato1

This page was generated on 2016-06-07 15:21:04 -0700 (Tue, 07 Jun 2016).

Package 184/1209HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.17.0
Oscar Reina
Snapshot Date: 2016-06-06 16:20:08 -0700 (Mon, 06 Jun 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chroGPS
Last Changed Rev: 117081 / Revision: 118222
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 1.17.0
Command: rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.17.0.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.17.0.tar.gz
StartedAt: 2016-06-07 02:28:15 -0700 (Tue, 07 Jun 2016)
EndedAt: 2016-06-07 02:32:03 -0700 (Tue, 07 Jun 2016)
EllapsedTime: 227.5 seconds
RetCode: 0
Status:  OK  
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.17.0.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/chroGPS.Rcheck'
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '1.17.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'chroGPS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Missing or unexported object: 'changepoint::cpt.method'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addVar: no visible global function definition for 'lm'
addVar: no visible global function definition for 'fitted'
addVar: no visible global function definition for 'arrows'
addVar: no visible global function definition for 'text'
boostMDS: no visible global function definition for 'cmdscale'
boostMDS : targetf: no visible global function definition for 'dist'
boostMDS: no visible global function definition for 'dist'
boostMDS: no visible global function definition for 'lm'
chisqdist : <anonymous> : <anonymous>: no visible global function
  definition for 'Rle'
chisqdist2: no visible global function definition for 'mclapply'
chisqdist2 : <anonymous> : <anonymous>: no visible global function
  definition for 'chisq.test'
contour2dDP: no visible global function definition for 'colors'
contour2dDP: no visible binding for global variable 'state'
contour2dDP: no visible binding for global variable 'na.omit'
contour2dDP: no visible global function definition for 'contour'
contour2dDP: no visible global function definition for 'filled.contour'
domainDist: no visible global function definition for 'boxplot'
getURL: no visible global function definition for 'download.file'
getmodEncodeBS: no visible global function definition for
  'download.file'
getmodEncodeBS: no visible global function definition for 'read.csv'
gffRead: no visible global function definition for 'read.table'
gps2xgmml: no visible global function definition for 'col2hex'
plotContour: no visible global function definition for 'contour'
premergeClusters: no visible global function definition for 'dist'
premergeClusters: no visible global function definition for 'points'
rdldist: no visible global function definition for 'installed.packages'
splitMDS: no visible global function definition for 'tail'
uniqueCount: no visible binding for global variable 'u'
xgmml2d: no visible global function definition for 'xmlOutputDOM'
xgmml2d: no visible global function definition for 'saveXML'
xgmml3d: no visible global function definition for 'xmlOutputDOM'
xgmml3d: no visible global function definition for 'saveXML'
clusGPS,distGPS-mds: no visible global function definition for
  'as.hclust'
clusGPS,distGPS-mds: no visible global function definition for 'hclust'
clusGPS,distGPS-mds: no visible global function definition for
  'as.dist'
clusGPS,distGPS-mds : <anonymous>: no visible global function
  definition for 'cutree'
distGPS,matrix: no visible global function definition for 'dist'
distGPS,matrix: no visible global function definition for 'mahalanobis'
gps2xgmml,mds: no visible global function definition for 'col2hex'
mds,distGPS-mds: no visible global function definition for 'dist'
mds,distGPS-missing: no visible global function definition for
  'cmdscale'
mds,distGPS-missing: no visible global function definition for
  'as.dist'
mds,distGPS-missing: no visible global function definition for 'dist'
mergeClusters,list: no visible global function definition for 'text'
mergeClusters,list: no visible global function definition for 'axis'
mergeClusters,list: no visible global function definition for 'points'
mergeClusters,list: no visible global function definition for 'abline'
plot,clusGPS-ANY: no visible global function definition for
  'weighted.mean'
plot,clusGPS-ANY: no visible global function definition for 'abline'
plot,clusGPS-ANY : <anonymous>: no visible global function definition
  for 'weighted.mean'
plot,clusGPS-ANY: no visible global function definition for 'rainbow'
plot,clusGPS-ANY: no visible global function definition for 'contour'
plot,mds-ANY: no visible global function definition for
  'terrain.colors'
plot,mds-ANY: no visible global function definition for 'text'
plot,mds-ANY: no visible global function definition for 'plot3d'
plot,mds-ANY: no visible global function definition for 'text3d'
plot,mds-ANY: no visible global function definition for 'spheres3d'
procrustesAdj,mds-distGPS: no visible global function definition for
  'dist'
Undefined global functions or variables:
  Rle abline arrows as.dist as.hclust axis boxplot chisq.test cmdscale
  col2hex colors contour cutree dist download.file filled.contour
  fitted hclust installed.packages lm mahalanobis mclapply na.omit
  plot3d points rainbow read.csv read.table saveXML spheres3d state
  tail terrain.colors text text3d u weighted.mean xmlOutputDOM
Consider adding
  importFrom("grDevices", "colors", "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "arrows", "axis", "boxplot",
             "contour", "filled.contour", "points", "text")
  importFrom("stats", "as.dist", "as.hclust", "chisq.test", "cmdscale",
             "cutree", "dist", "fitted", "hclust", "lm", "mahalanobis",
             "na.omit", "weighted.mean")
  importFrom("utils", "download.file", "installed.packages", "read.csv",
             "read.table", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'gplots'
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/chroGPS.Rcheck/00check.log'
for details.


chroGPS.Rcheck/00install.out:


install for i386

* installing *source* package 'chroGPS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'chroGPS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chroGPS' as chroGPS_1.17.0.zip
* DONE (chroGPS)

chroGPS.Rcheck/examples_i386/chroGPS-Ex.timings:

nameusersystemelapsed
addVar0.020.000.02
adjustPeaks000
boostMDS000
clusGPS-class000
clusGPS000
distGPS-class000
distGPS0.030.000.03
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml000
mds-class000
mds0.000.020.01
mergeClusters000
procrustesAdj2.010.273.51
profileClusters000
s20.520.000.52
splitDistGPS-class000

chroGPS.Rcheck/examples_x64/chroGPS-Ex.timings:

nameusersystemelapsed
addVar000
adjustPeaks000
boostMDS000
clusGPS-class000
clusGPS0.010.000.02
distGPS-class000
distGPS0.050.000.05
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml0.010.000.01
mds-class000
mds000
mergeClusters000
procrustesAdj2.820.233.20
profileClusters000
s20.440.030.46
splitDistGPS-class000